Phenotype and GWAS Information:

Agronomic Traits

Note: All the agronomic trait is from the article Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection.

Metabolic Traits

Note: All the metabolic trait is from the article Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism. Some metabolics have two replications, the second replication is end with '_2', like 'mr1002_2'.

Search Results:

The detailed information about mr1946 can be find at here.

GWAS Results:

Note: If the P-value of Linear Regression (LR) or Linear Mixed Model (LMM) ≤ 1e-5 or the rank ≤ 20000, the results are saved. Only the LMM results are plotted below.

Significant Candidate Loci (Lead SNP):

Variation IDVariation ID V6ChromosomePositionLR P-value LMM P-value
vg0410003663 sf0409994360 4 10003663 4.52E-09 9.16E-10
vg0410077726 sf0410068424 4 10077726 5.04E-09 7.64E-10
vg0406529240 sf0406524683 4 6529240 7.54E-09 1.56E-08
vg0407491126 sf0407486396 4 7491126 4.19E-08 4.08E-09
vg0407810542 sf0407805810 4 7810542 6.16E-08 1.68E-08
vg1216184823 sf1216182119 12 16184823 2.02E-07 8.58E-08
vg0412597650 sf0412588360 4 12597650 2.62E-07 1.67E-08
vg1205351745 sf1205350731 12 5351745 3.09E-07 4.21E-07
vg0502043743 sf0502043725 5 2043743 7.81E-07 2.46E-07
vg0628129354 sf0628128356 6 28129354 7.86E-07 3.06E-06
vg0403322252 sf0403317855 4 3322252 8.70E-07 2.47E-06
vg0116965632 sf0116964586 1 16965632 2.47E-06 2.79E-06
vg1216087306 sf1216084602 12 16087306 5.09E-06 3.02E-06
vg0326473364 sf0326466458 3 26473364 5.82E-06 NA
vg1115128374 sf1114664688 11 15128374 9.99E-06 3.60E-06
vg0209301301 sf0209301299 2 9301301 NA 3.69E-06